What does 'modified' mean in the Package history? If a package is updated during an update cycle, and there is no new
version/revision available, the package will be marked as 'modified'.
It will also be marked as 'modified' if the packages files has been
altered (DESCR, distinfo, PLIST, et cetera) or if the package was
requested for an unconditional update.

Why doesn't the packages creation date correspond with the CVS date? The original package history is not imported, thus the oldest date in
the pkgsrc.se database will be the first time it was imported into the
database. However, newly imported packages seems to correspond very
well with the CVS date.

Why is package 'abc123' missing from the site? If a package is missing, it might be due to it does not build properly.
Build errors will probably make the package disappear from http://pkgsrc.se

Can I see all the removed packages? Yes; packages does not get deleted for archive reasons, but a package
that is marked as removed will not appear in search results or in
category listings. They will appear if you give the full address of
the package though (http://pkgsrc.se/CATEGORY/FOLDER).
All removed packages is browsable here.